That infuriated City players, who surrounded the referee, and the dispute spilled into the rival technical areas with Sergio Aguero having to be dragged away by Guardiola as he argued furiously with Wigan coaches.
In an uncanny repeat of the 2013 FA Cup final, in which City had a player sent off before losing to a late Wigan victor, Guardiola's side had Fabian Delph dismissed amid stormy scenes before Will Grigg's 79th-minute goal decided the game.
City's anger over Delph's dismissal may have been sparked because referee Anthony Taylor initially took out his yellow card, suggesting a booking, but then brandished the red.
The 79th-minute goal stunned City, who were unable to create a killer chance to rescue their hopes of winning every competition this season.
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Ankara considers the YPG to be an arm of the PKK, a banned Kurdish group that has waged a decades-long insurgency in Turkey. Turkish President Tayyip Erdogan meets US Secretary of State Rex Tillerson in Ankara , Turkey February 15, 2018.
Although Stones feels the red card had an impact, he maintains the runaway Premier League leaders did enough at least to force a replay.
It was otherwise a very strong City side that Wigan overcame, but Guardiola had no complaints over his team's efforts. They had one shot on target, I don't have regrets with the way we played, the performance, the heart.
The victory sparked wild celebrations by Latics supporters and they invaded the pitch on the final whistle. It's not really right what has gone on but it's the emotions of football.
"In addition, both clubs have been asked to provide their observations following the crowd trouble at the end of the game and have until Monday, Feb. 26 to respond".
The FA is expected to conduct their own investigation into the incident involving Aguero, who was seen lashing out at the fan as Wigan defender Chey Dunkley tried to calm the situation.
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"I don't think it will detract from our victory - not one bit". Stay with us throughout the day for more as we prepare for Sunday's Wembley showdown.
Argentine striker Aguero was among those taunted by several fans and footage shown by the BBC captured him appearing to hit out at a man in a green jacket.
"They've got some unbelievable players, some of the best players in the world and we defended unbelievably well".
"It's not great", he said.
Cook said: "We had to dig in, we really did, and the lads did that in abundance".
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The victor will advance to the final of the tournament but more than that, will mark himself out as the top dog in the division. His opponent George Groves is available at 6/4 to complete the biggest victory of his short, but esteemed career thus far.